You can discontinue the doxycycline or reduce the dosage. Adding lactobacillus is a good option and there are combination tablet available with lactobacillus. There are different ways to achieve a flawless skin after acne and it needs medical interventions. Acne treatment has multiple stages - to control new breakouts, to clear the sequalae (pigmentation and scars) and to prevent a relapse. If you have active acne lesions, it should be controlled on priority basis. Acne scar and pores can be treated with subcision, dermaroller, fractional CO2 lasers, chemical peels and likewise. Remember combining treatment modalities help to achieve desired results earlier. Your dermatologist will decide a treatment plan for you after a consultation.